"At the same time it will also open up over 90 global destinations for Cape Town’s travellers who can now avoid travelling via Johannesburg."
Cape Town is the Dubai-based airline's 100th destination.
The inaugural flight had passengers from 18 countries some coming from as far as the United States, France, Germany, Poland, Kuwait, Bahrain, India and Pakistan, as the United Arab Emirates.
Emirates says it already flies to Johannesburg 21 times a week, with a new daily service added last year. The Cape Town service represents 2,000 seats and more than 100 tonnes of cargo capacity a week.
Emirates is one of the fastest growing airlines in the world.
The airline says it is starting new services to Calicut, India